Re: [galaxy-dev] Trouble linking to/displaying at local Genome Browser
Hi Josh, Correct, to get the display functionality to work, your first two steps are sufficient. The other steps are only needed if you want to allow users to use your local mirror as a data source inside of Galaxy. If you don't want users to be able to use your local mirror as a data source, which may have faster loading times or additional data loaded that does not exist in UCSC's public site, you can safely remove the entry from your tool_conf.xml file without affecting the ability for your users to send files for display. Thanks for using Galaxy, Dan On Feb 27, 2012, at 1:13 PM, Josh Nielsen wrote: > One more thing while I'm at it. For clarification would only the first two > steps I listed be sufficient to get the "display at" link in Galaxy? If so > what is the benefit of the other steps (other than having an actual link to > your local genome browser mirror in Galaxy)? There's nothing that ties my > internalgb entry to the new tool_id I created is there? > > > On Mon, Feb 27, 2012 at 11:58 AM, Josh Nielsen > wrote: > Hi Dan, > > Good catch sir! Genius! It is working now. The spacing was exactly the same > to the eye in vi for all the entries, but once I did a 'set list' in vi to > display formatting characters I saw that 'main' had the tab ^I characters but > my 'internalgb' entry didn't. This must have happened because I did a "visual > copy" with my cursor. Thank you. > > -Josh > > On Mon, Feb 27, 2012 at 11:09 AM, Daniel Blankenberg wrote: > Hi Josh, > > It sounds like you are really close to getting this to work. My first guess > would be that there is an issue with the modified ucsc_build_sites.txt file. > Can you check that the line you copied is tab delimited and not space > delimited? > > > Thanks for using Galaxy, > > Dan > > On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote: > >> Hello all, >> >> I am having some trouble getting a "display at" link to my local UCSC Genome >> Browser mirror to show up under my Galaxy jobs for viewing, although I can >> get the link to the online UCSC GB to display. I followed the suggestions in >> the following thread but it has yielded no results yet: >> http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html. >> >> Here's what I have tried: >> - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file >> and duplicated the 'main' UCSC entry but changed the new entry's name to >> 'internalgb' and changed the URL to point to our local GB with >> cgi-bin/hgTracks? at the end >> - I set "ucsc_display_sites = internalgb" in universe_wsgi.ini >> - I made a modified copy of >> [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named >> HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and >> created a tool link on the left side of the Galaxy page for it by adding it >> to the tool_conf.xml file (which works fine: when I click on it it loads our >> local Genome Browser inside the central Galaxy window frame) >> - I edited the HAIB_ucsc_tablebrowser.xml file according to the >> recommendation in the thread above: "I had to change the name and id of the >> tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the >> param.toold_id.value as well." So I gave it a unique id (changed >> ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field >> the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I >> put the new HAIB id for our local tablebrowser into universe_wsgi.ini under >> the tool runners section as "HAIB_table_direct1 = local:///" >> - And of course I have restarted Galaxy after each change. >> >> Still after all of this I cannot see a "display at" link for bam & other >> files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to >> have "ucsc_display_sites = internalgb,main" set (for both browsers) the >> online/main GB will have a "display at" link on Galaxy jobs but no link >> shows for my local browser mirror. I'm also a little fuzzy on the relation >> between the ucsc_build_sites.txt file and the "*_ucsc_tablebrowser.xml" >> files (if any). Any tips as to what I might be missing here? >> >> Thanks! >> Josh >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Trouble linking to/displaying at local Genome Browser
One more thing while I'm at it. For clarification would only the first two steps I listed be sufficient to get the "display at" link in Galaxy? If so what is the benefit of the other steps (other than having an actual link to your local genome browser mirror in Galaxy)? There's nothing that ties my internalgb entry to the new tool_id I created is there? On Mon, Feb 27, 2012 at 11:58 AM, Josh Nielsen wrote: > Hi Dan, > > Good catch sir! Genius! It is working now. The spacing was exactly the > same to the eye in vi for all the entries, but once I did a 'set list' in > vi to display formatting characters I saw that 'main' had the tab ^I > characters but my 'internalgb' entry didn't. This must have happened > because I did a "visual copy" with my cursor. Thank you. > > -Josh > > On Mon, Feb 27, 2012 at 11:09 AM, Daniel Blankenberg wrote: > >> Hi Josh, >> >> It sounds like you are really close to getting this to work. My first >> guess would be that there is an issue with the modified >> ucsc_build_sites.txt file. Can you check that the line you copied is tab >> delimited and not space delimited? >> >> >> Thanks for using Galaxy, >> >> Dan >> >> On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote: >> >> Hello all, >> >> I am having some trouble getting a "display at" link to my local UCSC >> Genome Browser mirror to show up under my Galaxy jobs for viewing, although >> I can get the link to the online UCSC GB to display. I followed the >> suggestions in the following thread but it has yielded no results yet: >> http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html >> . >> >> Here's what I have tried: >> - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt >> file and duplicated the 'main' UCSC entry but changed the new entry's name >> to 'internalgb' and changed the URL to point to our local GB with * >> cgi-bin/hgTracks?* at the end >> - I set "*ucsc_display_sites = internalgb*" in universe_wsgi.ini >> - I made a modified copy of >> [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml >> (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other >> XML files and created a tool link on the left side of the Galaxy page for >> it by adding it to the tool_conf.xml file (which works fine: when I click >> on it it loads our local Genome Browser inside the central Galaxy window >> frame) >> - I edited the HAIB_ucsc_tablebrowser.xml file according to the >> recommendation in the thread above: "*I had to change the name and id of >> the tool in the new ucsc_tablebrowser.xml file, and keep the id the same >> for the param.toold_id.value as well*." So I gave it a unique id >> (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id >> value field the same as the original/main UCSC tablebrowser (u >> csc_table_direct1). Then I put the new HAIB id for our local >> tablebrowser into universe_wsgi.ini under the tool runners section as >> "*HAIB_table_direct1 >> = local:///*" >> - And of course I have restarted Galaxy after each change. >> >> Still after all of this I cannot see a "display at" link for bam & other >> files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini >> to have "ucsc_display_sites = internalgb,main" set (for both browsers) >> the online/main GB will have a "display at" link on Galaxy jobs but no link >> shows for my local browser mirror. I'm also a little fuzzy on the relation >> between the ucsc_build_sites.txt file and the "*_ucsc_tablebrowser.xml" >> files (if any). Any tips as to what I might be missing here? >> >> Thanks! >> Josh >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> >> > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Trouble linking to/displaying at local Genome Browser
Hi Dan, Good catch sir! Genius! It is working now. The spacing was exactly the same to the eye in vi for all the entries, but once I did a 'set list' in vi to display formatting characters I saw that 'main' had the tab ^I characters but my 'internalgb' entry didn't. This must have happened because I did a "visual copy" with my cursor. Thank you. -Josh On Mon, Feb 27, 2012 at 11:09 AM, Daniel Blankenberg wrote: > Hi Josh, > > It sounds like you are really close to getting this to work. My first > guess would be that there is an issue with the modified > ucsc_build_sites.txt file. Can you check that the line you copied is tab > delimited and not space delimited? > > > Thanks for using Galaxy, > > Dan > > On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote: > > Hello all, > > I am having some trouble getting a "display at" link to my local UCSC > Genome Browser mirror to show up under my Galaxy jobs for viewing, although > I can get the link to the online UCSC GB to display. I followed the > suggestions in the following thread but it has yielded no results yet: > http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html > . > > Here's what I have tried: > - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt > file and duplicated the 'main' UCSC entry but changed the new entry's name > to 'internalgb' and changed the URL to point to our local GB with * > cgi-bin/hgTracks?* at the end > - I set "*ucsc_display_sites = internalgb*" in universe_wsgi.ini > - I made a modified copy of > [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml > (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML > files and created a tool link on the left side of the Galaxy page for it by > adding it to the tool_conf.xml file (which works fine: when I click on it > it loads our local Genome Browser inside the central Galaxy window frame) > - I edited the HAIB_ucsc_tablebrowser.xml file according to the > recommendation in the thread above: "*I had to change the name and id of > the tool in the new ucsc_tablebrowser.xml file, and keep the id the same > for the param.toold_id.value as well*." So I gave it a unique id (changed > ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value > field the same as the original/main UCSC tablebrowser (ucsc_table_direct1). > Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini > under the tool runners section as "*HAIB_table_direct1 = local:///*" > - And of course I have restarted Galaxy after each change. > > Still after all of this I cannot see a "display at" link for bam & other > files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini > to have "ucsc_display_sites = internalgb,main" set (for both browsers) > the online/main GB will have a "display at" link on Galaxy jobs but no link > shows for my local browser mirror. I'm also a little fuzzy on the relation > between the ucsc_build_sites.txt file and the "*_ucsc_tablebrowser.xml" > files (if any). Any tips as to what I might be missing here? > > Thanks! > Josh > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Trouble linking to/displaying at local Genome Browser
Hi Josh, It sounds like you are really close to getting this to work. My first guess would be that there is an issue with the modified ucsc_build_sites.txt file. Can you check that the line you copied is tab delimited and not space delimited? Thanks for using Galaxy, Dan On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote: > Hello all, > > I am having some trouble getting a "display at" link to my local UCSC Genome > Browser mirror to show up under my Galaxy jobs for viewing, although I can > get the link to the online UCSC GB to display. I followed the suggestions in > the following thread but it has yielded no results yet: > http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html. > > Here's what I have tried: > - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file > and duplicated the 'main' UCSC entry but changed the new entry's name to > 'internalgb' and changed the URL to point to our local GB with > cgi-bin/hgTracks? at the end > - I set "ucsc_display_sites = internalgb" in universe_wsgi.ini > - I made a modified copy of > [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named > HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and > created a tool link on the left side of the Galaxy page for it by adding it > to the tool_conf.xml file (which works fine: when I click on it it loads our > local Genome Browser inside the central Galaxy window frame) > - I edited the HAIB_ucsc_tablebrowser.xml file according to the > recommendation in the thread above: "I had to change the name and id of the > tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the > param.toold_id.value as well." So I gave it a unique id (changed > ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field > the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I > put the new HAIB id for our local tablebrowser into universe_wsgi.ini under > the tool runners section as "HAIB_table_direct1 = local:///" > - And of course I have restarted Galaxy after each change. > > Still after all of this I cannot see a "display at" link for bam & other > files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to > have "ucsc_display_sites = internalgb,main" set (for both browsers) the > online/main GB will have a "display at" link on Galaxy jobs but no link shows > for my local browser mirror. I'm also a little fuzzy on the relation between > the ucsc_build_sites.txt file and the "*_ucsc_tablebrowser.xml" files (if > any). Any tips as to what I might be missing here? > > Thanks! > Josh > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Trouble linking to/displaying at local Genome Browser
Hello all, I am having some trouble getting a "display at" link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html . Here's what I have tried: - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file and duplicated the 'main' UCSC entry but changed the new entry's name to 'internalgb' and changed the URL to point to our local GB with * cgi-bin/hgTracks?* at the end - I set "*ucsc_display_sites = internalgb*" in universe_wsgi.ini - I made a modified copy of [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and created a tool link on the left side of the Galaxy page for it by adding it to the tool_conf.xml file (which works fine: when I click on it it loads our local Genome Browser inside the central Galaxy window frame) - I edited the HAIB_ucsc_tablebrowser.xml file according to the recommendation in the thread above: "*I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well*." So I gave it a unique id (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini under the tool runners section as "*HAIB_table_direct1 = local:///*" - And of course I have restarted Galaxy after each change. Still after all of this I cannot see a "display at" link for bam & other files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to have "ucsc_display_sites = internalgb,main" set (for both browsers) the online/main GB will have a "display at" link on Galaxy jobs but no link shows for my local browser mirror. I'm also a little fuzzy on the relation between the ucsc_build_sites.txt file and the "*_ucsc_tablebrowser.xml" files (if any). Any tips as to what I might be missing here? Thanks! Josh ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
